Variants of linked collection instances
I found it! According to docs library override doesn't work well with overriding animations. While I didn't actually animate turrets inside their file, I marked some properties (rotations) as properties for animation - that was enough to break the behavior of library override.



Docs:

https://docs.blender.org/manual/en/latest/files/linked_libraries/library_overrides.html#editing-an-override